[gmx-users] FEP from .top gathered with TOPOGROMACS from NAMD-CHARMM MD

Francesco Pietra chiendarret at gmail.com
Mon Jun 18 11:23:01 CEST 2018


I am new to GROMACS.

I would like to run ligand-protein absolute FEP simulations with
GROMACS-CHARMM36 ff. My aim is to compare with the same simulations I
carried out with NAMD-CHARMM36 ff.

I got the .top file inclusive of all parametrss via TOPOGROMACS. I plan to
obtain all necessary files to first continue MD equilibrations with GROMACS
by passing the NAMD equilibrated .pdb file and the .top file to GROMPP (I
am looking for direction on howto).

The thermodynamic cycle I used with NAMD is similar to the one in the 2016
GROMACS FEP tutorial. However,  I am rather confused on how to add flags
and restraints after the MD equilibration. With NAMD, FEP flags and
restraints are simply added to the general MD configuration file.

Thanks for advice.

francesco pietra

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